6WFI

Methylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JC5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729850 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.6 M ammonium sulfate, 5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
1.8634.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.837α = 90
b = 68.837β = 90
c = 103.37γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX300HEMD2 Micro Diffractometer2017-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.373099.80.0590.0590.0610.01614.214.252867-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.421000.470.476.51613.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JC51.3725.8650250254899.740.14860.14740.1736RANDOM19.115
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.190.19-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.574
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg12.545
r_dihedral_angle_1_deg7.452
r_angle_refined_deg2.617
r_angle_other_deg1.653
r_chiral_restr0.287
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.574
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg12.545
r_dihedral_angle_1_deg7.452
r_angle_refined_deg2.617
r_angle_other_deg1.653
r_chiral_restr0.287
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1109
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms74

Software

Software
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction